CLI and config file should be decoupled

[LiamPattinson]

PR #232 introduces per-file-ignores, which have the following syntax on the command line:

--per-file-ignores=<pattern>:<ignore>
# e.g.
--per-file-ignores=**/some_dir/*.f90:typing,**/some_dir/*.f90:style

As the config file is read using serde and the same structs used by clap to define the CLI, the same syntax is needed in the config files:

[check]
per-file-ignores = [
  "**/some_dir/*.f90:typing",
  "**/some_dir/*.f90:style",
]

A better syntax, and one familiar to Ruff users, would be:

[check.per-file-ignores]
"**/some_dir/*.f90" = ["typing", "style"]

As more configuration options are added there will likely be more instances where the best practices for the CLI and config files will diverge, and so we should implement a separate set of structs for the config files.